Exercise for 10/9/2006

Last week we assembled a database designed to study Cnidarians. This week we will use that database to find out if Cnidarians have homeobox genes. Retrieve the sequences listed below from NCBI and blast them against your database. Blast them one at a time against your database. Retrieve the top cnidarian hit for each of the queries and answer the following questions.

What are the highest quality hits to cnidarian sequences? Make sure they are actually cnidarian.

Do the sequences align well along their entire length? Try to do your global alignment from the command line. You can find the correct program in /opt/local/bin. The hardest part is getting the path correct. You may need to put in the entire path from the root. What is the percent similarity if the sequences are aligned along their entire length?

If they only align along a limited region, what do you think this part of the sequence does? Is there a way you can test this? Try looking through the options on the blast page at NCBI?

Try these sequences:
NM_001075313.1
NM_206006.2
AK227423.1

Read:

man man
man ls
man tcsh
man bash


You can avoid having to repeated type in complex paths by judicious use of aliases and file linking. If you routinely use a set of software that you have installed, you may also wish to create a sub-directory in your home directory that contains executable code and is within your path. For example, you might wish to create a directory:

~/bin

"~" at the beginning of a unix path will refer to the users home directory, so that is equivalent to ~myhomedirectory/bin.

And within that directory create links to the binaries you wish to use:

ln -s /opt/bin/hairypath/evenharierpath/stillmorehairypath/tofilenameicouldneverremember.bin ~/bin/easyfilename

Now if you do

ls ~/bin

you will see that a file named "easyfilename" has been created; you can use this instead of the much harder to remember full path.

If you do:

ls -l ~/bin

You will see that that file is a link (and will get a bunch of other useful information about it).

Advanced:

You may also wish to add ~/bin to your path. In this case, executable files will automatically be found. However, setting a path correctly is a bit awkward, and if you incorrectly set your path it will make it *much* more difficult to use the computer. So if you decide to do this, be sure you have the syntax right, and don't put it into your .cshrc until you are absolutely certain you have the command correct.

 

(Written by John Miller, modified by Charles Delwiche)